The Technology Core will support all four Research Projects by providing a broad range of next-generation sequencing and data analysis capabilities. Core functions are divided into sequencing, primary data analysis, and comparative analysis. Sequencing strategies will include whole genome and targeted sequencing, transcriptome profiling by RNA-seq, rRNA profiling, and metagenomic and metatranscriptomic sequencing. Six different sequencing instrument platforms will be used including lllumina MiSeq and HiSeq, lon Torrent, ABI 3730x1, 454 FLX+, and Pacific Biosciences RSH. Sample tracking is managed throughout the process and extensive quality assessment is performed to maximize the yield of usable information. Ongoing evaluation of new methods will enable implementation of new approaches for library construction and sequencing, increase efficiency and lower costs. Automated pipelines are in place to handle most assembly, variant detection, and annotation tasks. Data analysis methods will be improved throughout the project to increase automation, improve results by incorporating new analytical methods, and provide more readily shared software, Comparative analysis will leverage PanOCT to identify shared and strain/clade-specific genome features. New methods will be developed for metatranscriptome analysis that enable quantitative comparisons between samples with and without reference genomes or metagenomes. The results of the Core will provide Research Projects with analyzed data that is suitable for further integrative analysis and interpretation. The Technology Core will work closely with the Data Management, Analysis and Resource Dissemination (DMARD) Core to ensure prompt submission of sequence data, clones, and software tools to the appropriate public repositories.